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Supercomputer Fights AIDS

The virtual supercomputer will test thousands of human immuno-deficiency virus (HIV) mutations against tens of thousands of chemical compounds.

K.C. Jones

November 21, 2005

3 Min Read

One of the world's most powerful computing systems is battling AIDS.

In the first research effort of its kind, World Community Grid is devoting massive computational powers to FightAIDS@Home.

IBM announced Monday that the virtual supercomputer will test thousands of human immuno-deficiency virus (HIV) mutations against tens of thousands of chemical compounds. That will help scientists design effective therapies to stop potential drug-resistant viral strains from causing AIDS, Vice President of IBM Global Initiatives Robin Willner said in an interview Monday.

"AIDS is the most potent and destructive scourge right now in terms of diseases," Willner said. "HIV can be stopped when people take drugs that prevent the virus from multiplying in the body, but it's particularly dangerous because it mutates and changes so quickly."

World Community Grid consists of more than 100,000 people donating unused time from 170,000 computers. The grid invites volunteers to download Rosetta software, which runs during idle time. The virtual supercomputer solves scientific problems and creates public databases for scientific research. To qualify for World Community Grid support, a project must hold potential for contributing to the greater good.

"AIDS is perhaps the most devastating epidemic of our time," Nobel Prize biologist and President of the California Institute of Technology David Baltimore said in a prepared statement. "Its growing impact on the developing nations of the world is both tragic and destabilizing. Through World Community Grid, individuals in all parts of the globe can participate in helping develop effective, inexpensive and robust therapies against HIV and potentially reverse the downward health and economic impacts of this epidemic."

A team of experts in molecular biology, bioinformatics software and molecular computer modeling have been working on the project with computational chemists, specialists in virology, and cell biology experts at The Scripps Research Institute in San Diego.

After two years with the Entropia computing environment, operators at the institute's Olson Laboratory decided to switch to World Community Grid. They said several features of Entropia did not work for them and newer versions of AutoDock could not be deployed.

By migrating to the more powerful infrastructure, they hope to reap several benefits.

"The new World Community Grid project will run millions upon millions of docking computations to evaluate potential interactions between compounds and mutant viral proteins," Anderson Research Chair Professor of Scripps' Department of Molecular Biology, Dr. Arthur J. Olson, said in a prepared statement.

IBM researchers have been preparing the World Community Grid for the AIDS research since August. The grid provides a discussion forum and increases awareness of the project. Donors can track their contributions and overall project statistics. A three-dimensional graphical output will display computational progress.

The infrastructure allows maintenance and updates of the science run on FightAIDS@Home as well as AutoDock. It will also support FightAIDS@Home on Linux based systems.

Project leaders hope to complete the calculations within a year.

Meanwhile, the grid's first major set of computations, through the Human Proteome Folding Project, are 99 percent done, according to Willner.

In the year since its launch, the grid performed about 120,000 simulations of protein folding patterns and produced a database for researchers. The work, which would have taken about 100 years for the Institute for Systems Biology's supercomputer to perform, shows scientists how amino acids fold into three-dimensional structures.

Proper folding is essential to protein functioning and ultimately health. So, understanding the folding process is a step toward understanding and curing diseases like cancer and malaria.

World Community Grid makes technology and scientific findings publicly available. It is only used for humanitarian research.

IBM donates the hardware, software, technical services and expertise to create the infrastructure for the grid. The company also provides free hosting, maintenance and support.

There are six other projects in the pipeline and all can run simultaneously, Willner said. IBM plans to announce several new philanthropic grid computing efforts in the first quarter of 2006.

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